I have to say that my opinion is to let DEVONthink 3 do it all. Obviously though BLUEFROG is right, as you guessed! I do make folders of obvious things now on import. Collections of papers on a very narrow topic for example. Even that is matter of opinion really though. In my case say ‘climate science’ merges with several other topics now, to my dismay in fact.
I just have a database for each part of the year, again no clear set boundary as to when I move to a new one and/or reimport the old files into that. Generally that pattern cleaves closely to my actual thinking and inquiry.
I basically use a pretty flat system, most stuff is a the top level with a few, now mostly historical, folders.
For example I have a paper which I copied using screenshots, it was very hard to download and inaccessible, so that sequence of screenshots has its own folder, I don’t hardly look at it nowadays anyway.
Then I use the search and smart rule functions on the flat organization. For example I have a smart rule that picks out my own notes an a particular topic, and indeed all my own notes, which include ones in “Finder”. Honestly I recommend trying it, it is a bit nerve wracking at first, but it worked for me and more like my own mind works. In fact it seems more like the old paper mountains where one, somehow, knew where things were all the same?
I really think over using folders and recreating Finder systems is not using DEVONthink 3 to its full capacity.